Issues

• Update citations advice

  tskit-dev/msprime#2476 · Filter by author jeromekelleher opened on Feb 5, 2026

• Mark record_migrations as legacy in the docs

  tskit-dev/msprime#2436 · Filter by author hyanwong opened on Dec 5, 2025
  1

• Gene Conversion not correct in SMCK

  bug
  tskit-dev/msprime#2399 · Filter by author hossam26644 opened on Aug 12, 2025
  5

• Improve lineage/smc(k) handling for GC events

  tskit-dev/msprime#2386 · Filter by author jeromekelleher opened on Jul 24, 2025

• Bug in Dirac coalescent with single lineage in a population

  bug
  tskit-dev/msprime#2380 · Filter by author jeromekelleher opened on Jul 23, 2025
  2

• Confusing docs reference to 3 flags

  documentation
  tskit-dev/msprime#2364 · Filter by author hyanwong opened on May 6, 2025

• Mass migration events at time zero are skipped

  bug
  tskit-dev/msprime#2353 · Filter by author nspope opened on Apr 9, 2025
  16

• How to simulate data for a demographic trajectory in conjection with a reference genome sequence or output whole DNA sequence?

  tskit-dev/msprime#2340 · Filter by author yzliu01 opened on Feb 28, 2025
  1

• sim_ancestry with initial state can produce invalid ts when mutations exist above the roots

  tskit-dev/msprime#2319 · Filter by author ShyamieG opened on Aug 28, 2024
  5

• Coalescent rate trajectory ignores a population's activation time

  tskit-dev/msprime#2289 · Filter by author apragsdale opened on Jul 6, 2024
  2

• Demography.from_demes(): ancestral population sizes and migration rates missing

  tskit-dev/msprime#2255 · Filter by author simonharnqvist opened on Feb 2, 2024
  6

• Save information about sweep in SweepGenicSelection model

  enhancement
  tskit-dev/msprime#2243 · Filter by author jeromekelleher opened on Dec 13, 2023
  6

• Illogical Lineage Counts in algorithms.py

  tskit-dev/msprime#2242 · Filter by author agushin101 opened on Dec 12, 2023
  8

• Computing likelihood for decapitated ARGs.

  enhancement
  tskit-dev/msprime#2235 · Filter by author GertjanBisschop opened on Dec 7, 2023

• CpG mutation models

  tskit-dev/msprime#2221 · Filter by author hyanwong opened on Nov 14, 2023
  4

• No Sweep Model for Spatially Structured Populations

  tskit-dev/msprime#2218 · Filter by author YuanboSong opened on Oct 31, 2023
  1

• Inconsistencies between algorithm.c and algorithm.py

  tskit-dev/msprime#2217 · Filter by author YuanboSong opened on Oct 31, 2023
  1

• Define global stopping condition

  tskit-dev/msprime#2158 · Filter by author jeromekelleher opened on Feb 21, 2023

• population-specific recombination rates?

  tskit-dev/msprime#2127 · Filter by author gtsambos opened on Nov 29, 2022
  10

• add stack_policy argument to SLiMMutationModel

  tskit-dev/msprime#2113 · Filter by author petrelharp opened on Sep 30, 2022
  3

• create snakemake wrapper for msp?

  enhancement
  tskit-dev/msprime#2104 · Filter by author andrewkern opened on Aug 10, 2022
  2

• Implement 2D stepping stone model

  enhancement
  tskit-dev/msprime#2100 · Filter by author connor-french opened on Aug 1, 2022
  3

• Add example working out NaN bits when working with multiple chromosomes

  tskit-dev/msprime#2087 · Filter by author jeromekelleher opened on Jul 4, 2022

• Rework sectioning in mutations page

  documentation
  tskit-dev/msprime#2084 · Filter by author jeromekelleher opened on Jul 1, 2022

• more than 100 populations in one event

  tskit-dev/msprime#2067 · Filter by author lea-guyon opened on Jun 10, 2022
  3